The metabolome comprises all metabolites in a biological organism, which constitute the end products of its gene expression. Metabolomics consists on the systematic study of the chemical fingerprints resulting from specific cellular processes or, more particularly, the study of an organism’s profile of low molecular weight metabolites. Thus, metabolomics is perhaps the ultimate level of post-genomic analysis as it can reveal changes in metabolite fluxes that are controlled by only minor changes within gene expression. Classical phytochemical approaches often comprised a rather tedious and time consuming process of isolation, dereplication of known substances, followed by structure elucidation and quantification. However, it is important to highlight that, in many situations, the effects of natural products are not due to a single compound, but to a mixture of related and unrelated ones. Thus, metabolomics provides an efficient tool for the quality control and authentication of medicines of natural origin, contributing as well to the characterization of different species. Several combined techniques have been applied in the measurements of intracellular metabolites, whether qualitative or quantitative, which reveal the biochemical status of the organism. This review offers an insight on the methods used in the metabolomics analysis (LC-MS, GC-MS, HPLC-DAD, NMR) of several natural matrices with protective health potential, with special emphasis on the determination of phenolics profiles, once these represent the most abundant and widely spread class of plant natural compounds, additionally exhibiting interesting biological activities.